commit: 0a17f05714124c90b425b51925dea9557a003422 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Mar 23 17:05:44 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Mar 23 17:05:44 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0a17f057
sci-biology/fastqc: a skeleton for a new perl wrapper calling java libs, need help Package-Manager: portage-2.2.7 --- sci-biology/fastqc/ChangeLog | 10 ++++++++++ sci-biology/fastqc/fastqc-0.10.1.ebuild | 29 +++++++++++++++++++++++++++++ sci-biology/fastqc/metadata.xml | 9 +++++++++ 3 files changed, 48 insertions(+) diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog new file mode 100644 index 0000000..69015c4 --- /dev/null +++ b/sci-biology/fastqc/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/fastqc +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*fastqc-0.10.1 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs <[email protected]> + +fastqc-0.10.1.ebuild, +metadata.xml: + sci-biology/fastqc: a skeleton for a new perl wrapper calling java libs, need + help diff --git a/sci-biology/fastqc/fastqc-0.10.1.ebuild b/sci-biology/fastqc/fastqc-0.10.1.ebuild new file mode 100644 index 0000000..5274554 --- /dev/null +++ b/sci-biology/fastqc/fastqc-0.10.1.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 eutils + +DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" +HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"; +SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip"; + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/picard + >=virtual/jrei-1.6" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/FastQC + +src_install(){ + dobin fastqc + + # TODO: need to compile java in uk/ac/babraham/FastQC/ + # and decide whether jbzip2-0.9.jar and sam-1.32.jar are standard java libs and from samtools or whetehr not +} diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/fastqc/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
